Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate WP_078430749.1 BK574_RS01735 ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >NCBI__GCF_002019605.1:WP_078430749.1 Length = 321 Score = 160 bits (405), Expect = 4e-44 Identities = 99/287 (34%), Positives = 166/287 (57%), Gaps = 7/287 (2%) Query: 42 LCIGFSVLT-ENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVA 100 + I FS+L+ +FA + N I +Q S +++A G T V+ DLS+G++ S+ V++ Sbjct: 28 IIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLS 87 Query: 101 MLVSLM--PQLGMLSVPAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVG 158 L++ P + L VP ++ G + G NGA+V K+ F+ TL T + G+ + Sbjct: 88 ALLAASGTPIIFCLLVP--IIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLT 145 Query: 159 NDSTIY-NPDIGFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEA 217 +T++ N GF F+G ++ +P L +I F +V + W+++ +T LG ++YA+GGN +A Sbjct: 146 GGATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKA 205 Query: 218 ARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTS 277 + +SGI + +A+ G+LA G + ++RL +A+ G + L+A AAV LG T Sbjct: 206 SEVSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTG-GDGFFLNAYAAVFLGMTI 264 Query: 278 FVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAV 324 G +I+GTL GA II +++NGL +L V Q II G +II A+ Sbjct: 265 VKNGVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIAL 311 Lambda K H 0.325 0.141 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 372 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 337 Length of database: 321 Length adjustment: 28 Effective length of query: 309 Effective length of database: 293 Effective search space: 90537 Effective search space used: 90537 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory